Linkage Analysis and Association Mapping QTL Detection Models for Hybrids Between Multiparental Populations from Two Heterotic Groups: Application to Biomass Production in Maize (Zea mays L.)

Identification of loci (QTL) involved in the variation of hybrid value is of key importance for cross-pollinated species such as maize (Zea mays L.). In a companion paper we illustrated a new QTL mapping population design involving a factorial mating between two multi-parental segregating populations. Six biparental line populations were developed from four founder lines in the Dent and Flint heterotic groups. They were crossed to produce 951 hybrids, evaluated for silage performances. Previously, a linkage analysis model that assumes each founder line carries a different allele was used to detect QTL involved in General and Specific Combining Abilities of hybrid value. This previously introduced model requires the estimation of numerous effects per locus, potentially affecting QTL detection power. Using the same design we compared this "Founder alleles" model to two more parsimonious models which assume that (i) identity in state at SNP alleles from the same heterotic group implies identity by descent at linked QTL ("SNP within-group" model) or (ii) identity in state implies identity by descent, regardless of population origin of the alleles ("Hybrid Genotype" model). This last model assumes biallelic QTL with equal effects in each group. It detected more QTL on average than the two other models but explained lower percentages of variance. The "SNP within-group" model appeared to be a good compromise between the two other models. These results confirm the divergence between the Dent and Flint groups. They also illustrate the need to adapt the QTL detection model to the complexity of the allelic variation, which depends on the trait, the QTL and the divergence between the heterotic groups.

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